Blood samples are extensively used for clinical diagnosis and in medical research. In many assay formats, the presence of certain components in blood can interfere with the assay and render the test results unreliable or unusable. Interference is typically manifested as an inhibition of chemical reactions in the assay that reduces the performance and compromises the integrity of the assay and its result.
Patient samples may be compromised in a clinical setting by conditions such as poor handling, haemolysis, icterus, or lipemia. It is for example well known that HIV patients, treated with protease inhibitors, often show increased triglyceride levels. Yet another example of a compromised sample is cadaveric samples, which are often tested before organ transplantation. Cadaveric samples can be very challenging for nucleic acid tests, due to their potentially inhibitory nature from lysed or degraded tissues.
Blood samples, or samples derived from whole blood, are often analyzed for a nucleic acid analyte by the Polymerase Chain Reaction (PCR), other Nucleic Acid Amplification Technologies (NAT), or other nucleic acid detection technologies. NAT and PCR-based diagnosis of disease, infections, and genetic variations, as well as forensic analysis and blood typing are well known. It is also known that contaminants or PCR inhibitory substances such as lipids, hemoglobin, bilirubin or frequently administered drugs and anticoagulants can interfere with the PCR assay.
PCR-based assays rely on amplification and detection of nucleic acids present in the blood samples. These reactions can be dramatically reduced or blocked by the presence of contaminants or natural components of blood that inhibit chemical or biochemical reactions that occur in the assay. Blood components known as PCR inhibitors include immunoglobulin, heme, hemoglobin, leukocyte DNA, and common blood additive such as the anticoagulant heparin. Therefore, the usefulness of PCR-based detection of microorganisms, pathogens and other targets in complex biological samples, such as clinical, environmental, and food samples, is limited in part by the presence of substances that inhibit the fundamental amplification reaction at PCR or which reduce the amplification efficiency.
Because the potential for contamination and interference in PCR-based assays is well known, a variety of different approaches have been studied to attempt to prevent the inhibition. In one approach, the inhibition caused by specific substances is tested to attempt to compensate for their presence in a test sample or assay.
Solutions that samples used for assays typically are, or may be, converted into a liquid form containing compounds that inhibit chemical or biochemical reactions in an assay. The agents that cause interference or inhibition in the inhibitory testing assay include: hemoglobin, L-ascorbic acid, free fatty acids, iron, heme, triglycerides, drugs, bilirubin, conjugated bilirubin, bicarbonate, pH extremes, proteins, bile acids, larger amounts of DNA, or keto-acids. These inhibitors may interfere with cell lysis, degrade or capture of the nucleic acids, inactivate Taq polymerase or degrade the specificity of this enzyme, or otherwise interfere with enzymes used in nucleic acid amplification or detection technologies. In particular reverse transcription PCR (rt-PCR), which initially reverse transcribes RNA into cDNA, is very sensitive to the presence of inhibitors. In an attempt to preserve the fidelity of the assay, different methods of sample preparation have been developed to remove the inhibitory effect of these blood-derived components.
It is possible to attempt to control for inhibitory substances by monitoring the presence or absence of PCR product(s) at the end of thermal cycling by gel electophoresis, dot blots, high-pressure liquid chromatography or microtiter or plate-based, calorimetric assay. The quantitative effect of inhibitors on DNA synthesis can also be studied by measuring the efficiency of incorporation of radiolabeled nucleotides. Recently, thermal cyclers with real-time detection of PCR product accumulation were introduced, offering a new possibility to study amplification efficiency and/or DNA synthesis efficiency. Most commonly a known amount of an internal control molecule, which should behave similar to the target, is added into each PCR reactions. A change from the expected signal generated by the internal control can indicate the presence of inhibitors but can also change if the assay was not performed correctly. An internal control used for quantification is sometimes referred to as Quantification Standard (QS).
A resolution of the problem of inhibiting substances in assays can be attempted by sample preparation techniques. PCR-inhibitory components include salts, complex polysaccharides, heme protein in blood, RNases, DNases, feces, some detergents (e.g., SDS), DNA intercalating substances (e.g., intercalating dyes), humic substances in soil, melanin, collagen, myoglobin, alcohol, calcium ions, lactoferrin, proteases, proteinases in milk, and urea in urine. Significant effort is being devoted to the development of sample preparation methods to remove these substances and overcome the problems of inhibition in the reactions that occur in an assay. Different processing techniques are also being employed to reduce the effect of inhibitors. For example, aqueous two phase-systems, boiling, density gradient centrifugation, dilution, DNA extraction methods, enrichment media, filtration, and immunological techniques have been used to attempt to avoid the effect of inhibitory substances in PCR analyses. The thermostable DNA polymerase is perhaps the most important target site of PCR-inhibiting substances. The most widely used polymerase in PCR-based methods for the detection of microorganisms is Taq DNA polymerase from Thermus aquaticus. Other DNA polymerases with manganese instead of magnesium as cofactor are commonly used for rt-PCR. Other systems use a reverse transcriptase in combination with a DNA polymerase for rtPCR. Taq DNA polymerase, as well as many other PCR enzymes, can be degraded by proteinases, denatured by phenol or detergents, and inhibited by blocking of the active site by the inhibitor, which is the effect of the heme protein Inhibitors can also work on the substrate by decaying DNA or RNA. RNases in plasma are known to destroy RNA, or DNases can destroy DNA.
One approach for quality control of analytical assays is to use a sample-processing control as an internal control to verify adequate processing of the target analyte. This monitors the presence of inhibitors to avoid a false negative result, or incorrect quantification. If the system fails with this control, then there is an invalid result.
While common interfering substances are well known, it remains difficult and inconvenient to prepare constant, quantified controls for analytical assays. The reliability of standard solutions may be questionable or concentrations may not be calculated correctly. Also, it is time-consuming to be constantly preparing standards and calibrating them from week to week. This is particularly true for clinical samples, where there is high volume of testing, yet these are samples which must conform to rigorous quality control standards. Further, patient samples may be contaminated, or be presented in less than optimum condition. Because sample size and availability may be limited, however, it is often important that these critical samples be accurately analyzed.
Known guidelines recognize two primary limitations of interference testing. Properties of compounds added to a serum pool may be different from those of the compound naturally circulating in vivo. Also, the presence of more than one interfering substance may offset or enhance the concentrations of interfering substance and analyte tested. Various combinations of interfering substances in various combinations, therefore, should be evaluated in an assay.
To assure optimum performance of the analytical assay, a test assay includes several types of controls in addition to the test sample. A negative control, usually with a key ingredient missing, indicates a positive test result can be trusted. A positive control, usually a known amount of the analyte of interest, indicates the assay is functional. An internal control has a known substance added to the test sample before analysis, while an external control compares the test sample with other samples of substances run in the same assay. Because analytical assays can be sensitive and are designed to detect very small quantities of analyte, it is very important to include complementary controls to evaluate an analytical assay for acceptance criteria.
Accepted guidelines for estimation of interference characteristics recommend evaluating the effect of potentially interfering substances added to the sample of interest, as well as evaluating the bias of individual patient specimens in comparison to a highly specific comparative measurement procedure (Clinical and Laboratory Standards Institute. Interference Testing in Clinical Chemistry; Approved Guideline—Second Edition, 2005, p. 13). An interference screen can be prepared by adding a potentially interfering substance to a sample pool and evaluating bias relative to a control portion of the same pool, which is termed paired-difference testing. An interference screen, with many substances at relatively high concentrations, simulates interference and provides a standardized evaluation to complement actual patient samples.
It would be very useful to have calibrated substances prepared in an interference panel to determine the presence of interfering substances and to evaluate the performance of an analytical assay. This would also allow the standardized comparison of interfering substances on different assays or diagnostic systems.